I've had it loads of times!
It's not any sort of mod behavior as far as I've observed, it's something coded into the stock game. If you look at your subsystems screen, on the top left hand side you should see a ticker that counts "Hull damage". Stock behavior (as far as I've noticed) is if that ticker is not 0, you will have those water pipes leaking until such a time as you return to port. There is no actual subsystem for that pipe.
The only solution I know of is to cut your war patrol short and head back to base for repairs if the damage is serious enough. Otherwise, I've had minor success with saving and then reloading the game, the water pipe leaks but with no sound.
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